cutadapt not found

[GaioTransposon]

Hi Samuel,

I used a newer version of nextflow these two ways:

NXF_VER=20.04.1 nextflow run \
    Golob-Minot/geneshot \
        --manifest test1.csv \
        --output output/ \
        -w work/ 

the above gave me this type of error:

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 4: cutadapt: command not found

(also after adding cutadapt manually and exporting the path to it) So I tried to install nextflow and cutadapt via a conda env like this:

conda create geneshot_env
conda activate geneshot_env
conda install nextflow=20.04.1

conda install -c bioconda nextflow=20.04.1
conda install -c bioconda cutadapt

nextflow run \
    Golob-Minot/geneshot \
        --manifest test1.csv \
        --output output/ \
        -w work/ 

same type of error as above. How do you have cutadapt installed ? Or any other suggestion?

Kind Regards Dany

[sminot]

The core problem that you are running into here is that Nextflow has not been instructed to use the Docker images provided for each task (which contain the executables for cutadapt and all other needed tools).

To help with issues like this, I have added some documentation to help you set up Nextflow in the right way for your computing resources.

https://github.com/Golob-Minot/geneshot/wiki/Execution-Backend

Let me know if any of this isn't clear, or if you run into any problems!